NM_001321623.1:c.-128-7622A>G

Variant names:

• chr2-201053215-T-C
• rs10469755
• NM_001321623.1:c.-128-7622A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321623.1(HYCC2):​c.-128-7622A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,810 control chromosomes in the GnomAD database, including 4,439 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4439 hom., cov: 31)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 6 publications found

Genes affected

HYCC2 (HGNC:28593): (hyccin PI4KA lipid kinase complex subunit 2) Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Predicted to be located in cytosol. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321623.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	NM_001321623.1	MANE Select	c.-128-7622A>G		intron	N/A	NP_001308552.1	A0A804HIT6
	HYCC2	NM_001321624.1		c.-31+18395A>G		intron	N/A	NP_001308553.1	A0A804HIT6
	HYCC2	NM_001321625.2		c.-128-7622A>G		intron	N/A	NP_001308554.1	A0A804HIT6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	ENST00000681958.1	MANE Select	c.-128-7622A>G		intron	N/A	ENSP00000507218.1	A0A804HIT6
	HYCC2	ENST00000418596.7	TSL:1	c.-128-7622A>G		intron	N/A	ENSP00000393667.2	Q8IXS8
	HYCC2	ENST00000286181.7	TSL:1	n.-128-7622A>G		intron	N/A	ENSP00000286181.3	F8W7X4

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32933 AN: 151692 Hom.: 4432 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00849

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.208

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.217 AC: 32976 AN: 151810 Hom.: 4439 Cov.: 31 AF XY: 0.213 AC XY: 15783 AN XY: 74190

African (AFR) AF: 0.375 AC: 15494 AN: 41350

American (AMR) AF: 0.164 AC: 2492 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3468

East Asian (EAS) AF: 0.00851 AC: 44 AN: 5170

South Asian (SAS) AF: 0.0709 AC: 341 AN: 4812

European-Finnish (FIN) AF: 0.165 AC: 1736 AN: 10536

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11528 AN: 67938

Other (OTH) AF: 0.206 AC: 433 AN: 2100

Alfa AF: 0.0583 Hom.: 63

Bravo AF: 0.227

Asia WGS AF: 0.0660 AC: 232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.51
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10469755; hg19: chr2-201917938;